To get the features into the GUI you can either submit them yourself to the FreePBX team or open a feature request on the issue tracker.
To solve the problem you have right now, it’s better to use the pjsip.endpoint_custom_post.conf to add your options on to the config that FreePBX produces.
If you set up a PJSIP extension 1000, which creates an endpoint named [1000], you can put in your pjsip.endpoint_custom_post.conf:
[1000](+)
rtp_timeout_hold=120
rtp_timeout=60
I believe this is better than locally modifying the PHP, which would get overwritten later by FreePBX updates.